The spike (S) protein of the recently emerged human coronavirus (MERS-CoV) mediates infection by binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). Here we mapped the receptor-binding domain in the S protein to a 231-amino acid fragment (residues 358-588) by evaluating the interaction of spike truncation variants with receptor expressing cells and soluble DPP4. Antibodies to this domain - much less so to the preceding N-terminal region - efficiently neutralize MERS-CoV infection.

The cognate motifs in the promoters are observed in only a subset of total genes across different domains of life. Hence, sequence-motif based promoter prediction may not be a holistic approach for whole genomes. Conversely, the DNA structural property, duplex stability is a characteristic of promoters and can be used to delineate them from other genomic sequences. In this study, we have used a DNA duplex stability based algorithm ‘PromPredict’ for promoter prediction in a broad range of eukaryotes, representing various species of yeast, worm, fly, fish, and mammal. Efficiency of the software has been tested in promoter regions of 48 eukaryotic systems. PromPredict achieves recall values, which range from 68 to 92% in various eukaryotes.

There is consensus that only a preventive vaccine can contain the HIV/AIDS pandemic. After 30 years still there is no preventive HIV vaccine. This article examines fundamental challenges to the development of a preventive HIV vaccine. They include the initially erroneous but powerful perception of the natural history of HIV disease, as an acute rather than a chronic illness even in the absence of therapy, the lack of appreciation of the quasispecies biology of HIV and the abandonment of principles of immunology theory caused by the allure of technological prowess. In addition two other important aspects are discussed: vaccines directed against transmitted/founder viruses (T/F) and the reconsideration of HIV inactivation as a viable means to obtain a preventive HIV vaccine using novel safe methods of inactivation not available during the early years of the pandemic.

Most viruses first encounter host cells at mucosal surfaces, which are typically colonized by a complex ecosystem of microbes collectively referred to as the microbiota. Recent studies demonstrate the microbiota plays an important role in mediating host–viral interactions and determining the outcomes of these encounters. This review outlines recently described examples of how bacteria and viruses impact each other particularly during infectious processes. Mechanistically, these effects can be broadly categorized as reflecting direct bacterial–viral interactions and/or involving microbial impacts upon innate and/or adaptive immunity.

Zaire and Sudan ebolavirus species cause a severe disease in humans and non-human primates (NHPs) characterized by high mortality rate. There are no licensed therapies or vaccines against Ebola virus disease (EVD), and the recent 2013-2016 outbreak in West Africa highlighted the need of EVD-specific medical countermeasures. Here, we have generated and characterized head-to-head the immunogenicity and efficacy of five vaccine candidates against Zaire ebolavirus (EBOV) and Sudan ebolavirus (SUDV) based on the highly attenuated poxvirus vector modified vaccinia virus Ankara (MVA), expressing either the virus glycoprotein (GP) or GP together with the virus protein 40 (VP40) forming virus-like particles (VLPs). In a human monocytic cell line the different MVA vectors (termed MVA-EBOVs and MVA-SUDVs) triggered robust innate immune responses, with production of beta interferon (IFN-β), pro-inflammatory cytokines, and chemokines. Additionally, several innate immune cells, such as dendritic cells, neutrophils, and natural killer cells were differentially recruited in the peritoneal cavity of mice inoculated with MVA-EBOVs. After immunization of mice with a homologous prime/boost protocol (MVA/MVA) total IgG antibodies against GP or VP40 from Zaire and Sudan were differentially induced by these vectors, which were mainly of the IgG1 and IgG3 isotypes. Remarkably, an MVA-EBOV construct co-expressing GP and VP40 protected chimeric mice challenged with EBOV to higher extend than a vector expressing GP alone. These results support the consideration of MVA-EBOVs and MVA-SUDVs expressing GP and VP40 and producing VLPs as best-in-class potential vaccine candidates against EBOV and SUDV.

Deleting a single gene from mosquitoes can make them highly resistant to the malaria parasite and thus much less likely to transmit the parasite to humans, according to a new paper from scientists at Johns Hopkins Bloomberg School of Public Health's Malaria Research Institute.

The amount of data being generated across the sciences and beyond is exploding. In physics, for example, a single research center, the European Organization for Nuclear Research (CERN), has produced more than 100 petabytes of data that must be stored for future generations of scientists. But standard media for archiving data, such as optical discs, hard drives, and magnetic tapes, have lifetimes of only a few years. In the search for better data storage technologies, DNA—the molecule that encodes biological information with remarkable longevity and enormous information density—has emerged as a promising storage medium. Writing in this issue, Organick et al.1 tackle concerns about whether DNA-based storage can be scaled up to large amounts of data. They use their newly developed protocol to store over 200 megabytes of digital information in DNA, and to retrieve the data with no errors. The scale of DNA information storage and retrieval is unprecedented, supporting suggestions that DNA may provide a reliable and compact alternative for archiving the world's data.

Single-cell genomics has unveiled the metabolic potential of dominant microbes inhabiting different environments, including the human body. The lack of genomic information for predominant microbes of the human body, such as bacteriophages, hinders our ability to answer fundamental questions about our viral communities. Here, we applied single-virus genomics (SVGs) to natural human salivary samples in combination with viral metagenomics to gain some insights into the viral community structure of the oral cavity. Results suggest a variable, complex, and interpersonal viral profile. Finally, we demonstrated the power of SVGs in combination with viral metagenomics to unveil the genetic information of the uncultured viruses of the human virome.

Scientists predicted that cacao trees may be extinct by 2050 due to factors including climate change, pests and fungal infections. To save chocolate, "the food of the gods", researchers within the chocolate industry is trying to use the innovative CRISPR genome editing technology to save these delicate plants. Genome editing for cacao is an effective way to build tougher cacao plants and help them survive the climate change. In fact, genetically modified chocolate is already on the market. Despite so, a chocolate deficit is still in our near future due to the increasing demand for it. Recently, the candy company, Mars, invested $1 billion into their "Sustainability Generation" R&D project and is teaming up with scientists to use the most effective genome editing tool, CRISPR/Cas9 technology, for editing and breeding stronger cacao plants. As part of their "Cocoa Sustainability Approach", Mars has already sequenced the cocoa genome and share their results to the public in 2013. With their new plan for making super chocolate, hopefully, we could avoid the predicted chocolate deficit from occurring.

Author summary Dengue virus (DENV) is a human pathogen transmitted by Aedes mosquitoes. Infection with DENV causes dengue fever and may develop into life-threatening dengue hemorrhagic fever. Dengue disease is increasing globally and current control methods are proving ineffective in curtailing this growing problem. A novel strategy to stop DENV transmission is currently being trialled in five countries through the introduction of Wolbachia, an insect endosymbiont, into wild Aedes aegypti populations. Various mechanisms have been proposed to explain Wolbachia-mediated virus blocking (WMVB) including the response of the host to Wolbachia and factors like cholesterol, immune genes and miRNAs. Here we followed the fate of virus in mosquito cell lines and found that Wolbachia does not alter virus binding or internalisation. Further tracking of the virus shows that its replication is reduced in the presence of Wolbachia. The reduced replication is associated with increased viral RNA degradation for both DENV and West Nile virus (WNV). Unlike earlier reports, we didn’t find any evidence for miRNA involvement in WMVB. Analysing the viral RNA further shows that the 3’ region of viral RNA is not fully degraded, indicating that the degradation is likely due to the cellular enzyme XRN1. Accumulation of DENV 3’ regions inhibited XRN1 in the absence of Wolbachia and reduced the activity of XRN1 but not in the presence Wolbachia. Knockdown of XRN1 using siRNA resulted in decreased WMVB associated with increased DENV RNA. The magnitude of WMVB is also dependent on the infectious virus dose and the intrinsic rate at which the virus strain replicates. Similar results were seen for different DENV serotypes confirming that slowly replicating viruses are blocked more efficiently by Wolbachia.

American higher education seems to be experiencing a kind of teaching renaissance. Articles on the subject proliferate on this site and others, suggesting a renewed interest and commitment to the subject across academe.

We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product.

The pathogenesis of multiple sclerosis (MS) has not been clarified. In addition to environmental factors; genetic determinants have been implicated in the pathogenesis of MS. Furthermore, endogenous retroviruses (ERV) might play a role in MS. The presence of oligoclonal immunoglobulin in cerebrospinal fluid (CSF) is a typical feature of MS. Recently, genetic polymorphisms in loci on human chromosomes 6, 14 and 18 have been identified as major determinants of CSF antibody levels in MS. The functional relevance of these single nucleotide polymorphisms (SNPs) remains unclear and none of them is located in an open reading frame. In previous studies, we identified ERV sequences in the vicinity of MS associated SNPs. Here, we describe the identification of ERV sequences in the neighborhood of SNPs associated with CSF antibody levels. All of the identified SNPs are located in the vicinity of ERV sequences. One of these sequences has very high homology to a sequence derived from the so-called MS-associated retrovirus (MSRV). Another cluster of three ERV sequences from the immunoglobulin heavy chain locus has retained the typical organization of retroviral genomes. These observations might shed new light on a possible association between ERVs and MS pathogenesis.

IDV infection has been associated with BRDC, one of the most devastating diseases of the cattle population. Moreover, with broad host range and high environmental stability, IDV has the potential to further gain virulence, or even infect humans. An efficacious vaccine is needed to prevent infection and stop potential cross-species transmission. In this study, we designed a DNA vaccine encoding the consensus HEF of two lineages of IDV (D/OK and D/660) and tested its efficacy in a guinea pig model. Our results showed that the consensus DNA vaccine elicited high-titer neutralizing antibodies and achieved sterilizing protection against two lineage-representative IDV intra-nasal infections. To our knowledge, this is the first study showing a DNA vaccine-expressing consensus HEF is efficacious in preventing different lineages of influenza D virus infections.

Serious scientific games are games whose purpose is not just fun. In the field of science, the serious goals include crucial activities for scientists: outreach, teaching and research. The number of serious games is increasing rapidly, in particular citizen science games (CSGs), games that allow people to produce and/or analyze scientific data. It is possible to build a set of rules providing a guideline to create or improve serious games. We present arguments gathered from our own experience (Phylo, DocMolecules, the HiRE-RNA contest and Pangu) as well as examples from the growing literature on scientific serious games.

Researchers have long known that RNA viruses called coronaviruses cause the common cold and pneumonia. In the last two decades or so, though, researchers have found that these viruses can jump between animal and human hosts. In recent years, coronaviruses have caused lethal outbreaks of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) that span multiple continents. To date, no retroviral drug has been approved to treat these infections.

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